a) Teza de abilitare: 1. Paun, Finite Automata, Unconventional Computing and Systems Biology, Universitatea din Bucuresti, 2012 b) Teza de doctorat: 2. A. Paun, Unconventional models of computation: DNA and membrane computing, (Modele neconventionale de calculabilitate: calculatoare pe baza de ADN si membrane), Ph.D. thesis, University of Western Ontario printing press, 2003. c) Brevete de inventie d) Carti, si capitole in carti 3. R. Freund, O. Ibarra, A. Paun, P. Sosik, H-C. Yen, Catalytic P systems, capitolul 4 in Membrane Computing Handbook, Oxford University Press, 2010, ISBN: 978-0-19-955667- 0. 4. O.H Ibarra, A. Leporati, A. Paun, S. Woodworth, Spiking Neural P Systems: Characterizations and Complexity, capitolul 13 in Membrane Computing Handbook, Oxford University Press, 2010, ISBN: 978-0-19-955667-0. 5. A. Paun, M. Paun, Analiza Statistica Folosind Limbajul R, Editura Matrix, Bucuresti, 189 pagini, 2009, ISBN: 973-755-514-4. 6. A. Paun, Computability of the DNA and Cells: Splicing and Membrane Computing, SBEB Publishing, 378 pagini, 2008, ISBN: 978-0-9802368-4-2. 7. A. Paun, I. Stanciu, A. Bancila, B. Popa, Calculabilitatea pe baza de membrane si proteine, capitol de carte in Bioinformatica vol II, Editura Tehnica, 131 pagini, 2008, ISBN: 978-973- 31-2342-2. 8. O.H. Ibarra, A. Paun, Membrane Systems: A Natural Way of Computing with Cells, book chapter (chapter 3, 26 pages), in S. Rajasekaran, J.Reif, eds., Handbook of Parallel Computing: Models, Algorithms and Applications (Chapman & Hall/Crc Computer & Information Science Series), 2007, ISBN: 978-1584886235. 9. S. Yu, A. Paun, eds., Implementation and Application of Automata, Lecture Notes in Computer Science 2088, Springer-Verlag, Berlin, 2001. ISBN: 978-3540424918. e) Lucrari referite in jurnale internationale (aproape toate sunt cotate ISI): (in bold sunt evidentiati studentii mei) 10. P. Sosík, A. Paun, A. Rodríguez-Patón: P systems with proteins on membranes characterize PSPACE. Theoretical Computer Science, vol. 488 (2013), 78-95. 11. A Paun, M. Paun, A. Rodríguez-Patón, M. Sidoroff: P Systems with proteins on Membranes: a Survey. Int. J. Found. Comput. Sci., vol. 22, iss. 1 (2011), 39-53. 12. J. Jack, A. Paun, A. Rodríguez-Patón: A review of the nondeterministic waiting time algorithm. Natural Computing, vol. 10, iss.1 (2011), 139-149. 13. J. Jack, A. Paun: Discrete Modeling of Biochemical Signaling with Memory Enhancement. T. Comp. Sys. Biology 11: (2009), 200-215. 14. O.H. Ibarra, A. Paun, A. Rodriguez-Paton, Sequential SNP systems based on min/max spike number, Theoretical Computer Science, vol. 410, iss. 30-32 (2009), 2982-2991.
15. A. Paun, M. Paun, A. Rodriguez-Paton, On the Hopcroft's minimization technique for DFA and DFCA, Theoretical Computer Science, vol. 410, iss. 24-25 (2009), 2424-2430. (jurnal ISI) 16. J. Jack, A. Paun, F A. Rodriguez-Paton, Discrete nondeterministic modeling of the FAS pathway, International Journal of Foundations of Computer Science, vol. 19 (October 2008), no. 5, pp. 1147-1162. 17. H. Chen, M. Ionescu, T.O. Ishdorj, A. Paun, Gh.Paun, M. Pérez-Jiménez, Spiking neural P systems with extended rules: universality and languages. Nat. Comput. 7 (2008), no. 2, pp. 147-166. 18. O.H. Ibarra, A. Paun, Computing with Cells: Membrane Systems - Some Complexity Issues, International Journal of Parallel, Emergent and Distributed Systems, 23:5, 2008, pp. 347-365 19. O.H. Ibarra, S. Woodworth, F. Yu, A. Paun, On spiking neural P systems and partially blind counter machines. Nat. Comput. 7 (2008), no. 1, pp. 3 19. 20. A. Paun, Gh. Paun, Small universal spiking neural P systems, BioSystems, 90 (1), 2007, pp. 48-60. 21. S. Cheruku, A. Paun, F.J. Romero-Campero, M.J. Perez-Jimenez, O.H. Ibarra; Simulating FAS-induced apoptosis by using P systems. Progress in Natural Science, 17(4), 2007, pp. 424-431. 22. O. H. Ibarra, A. Paun, Gh. Paun, A. Rodríguez-Patón, P. Sosík, S. Woodworth; Normal forms for spiking neural P systems. Theoretical Computer Science 372(2-3), 2007, pp. 196-217 23. A. Paun, B. Popa; P Systems with Proteins on Membranes. Fundamenta Informaticae, 72(4), 2006, pp. 467-483. 24. C. Campeanu, A. Paun, J.R. Smith, Incremental construction of minimal deterministic finite cover automata. Theoretical Computer Science, 363(2), 2006, pp. 135-148 25. R. Freund, M. Oswald, A. Paun, Optimal Results for the Computational Completeness of Gemmating (Tissue) P Systems, International Journal of Foundations of Computer Science, 16(5), 2005, pp. 929-942. 26. C. Campeanu, L. Kari, A. Paun, Results on Transforming NFA into DFCA, Fundamenta Informaticae, Vol 64, 2005, pp. 53-63. 27. R. Freund, A. Paun, P systems with active membranes and without polarizations, Journal of Universal Computer Science and Soft Computing, 9 (9), 2005, pp. 657-663. 28. S.N. Krishna, A. Paun, Results on Catalytic and Evolution-Communication P Systems, New Generation Computing, 22(4), 2004, pp. 377-394. 29. C. Campeanu, A. Paun, Counting the Number of Minimal DFCA Obtained by Merging States, International Journal of Foundations of Computer Science, 14(6), 2003, pp. 995-1006. 30. R. Belu, A. Paun, A. Belu, Neural Networks in Instrumentation, Measurement and Control, Romanian Journal of Information Science and Technology, 6(1-2), 2003, pp. 61-85. (jurnal ISI) 31. M. Ionescu, C. Martín-Vide, A. Paun, Gh. Paun, Unexpected universality results for three classes of P systems with symport/antiport, Natural Computing, Vol. 2, issue 4, 2003, pp. 337-348. 32. A. Paun, Gh. Paun, G. Rozenberg, Computing by Communication in Networks of Membranes, International Journal of Foundations of Computer Science, Vol. 13, No. 6 (2002), pp. 779-798. 33. C. Martin-Vide, A. Paun, G. Paun, G. Rozenberg, Membrane Systems with Coupled Transport: Universality and Normal Forms, Fundamenta Informaticae, 49, 1-3 (2002), pp. 1-15.
34. C. Martin-Vide, A. Paun, G. Paun, On the Power of P Systems with Symport Rules. J. UCS 8(2): pp. 317-331 (2002) 35. A. Paun, Gh. Paun, The Power of Communication: P Systems with Symport /Antiport, New Generation Computing, 20, 3 (2002), pp. 295-305. 36. A. Paun, P Systems with Global Rules, Theory Comput. Systems, 35, (2002), pp. 471-481. 37. C. Campeanu, A. Paun, S. Yu, An Efficient Algorithm for Constructing Minimal Cover Automata for Finite Languages, International Journal of Foundations of Computer Science, 13, 1 (2002), pp. 83-97. 38. A. Paun, On P Systems with Partial Parallel Rewriting, Romanian Journal of Information Science and Technology, 4, 1-2 (2001), pp. 203-210. 39. A. Paun, On the Diameter of Various Classes of H Systems, J. Automata, Languages and Combinatorics, 5, 3 (2000), pp. 315-324. 40. A. Paun, On Time-Varying H systems, Bulletin of the EATCS, 67 (1999), pp. 157-164. 41. A. Paun, Controlled H Systems of a Small Radius, Fundamenta Informaticae, 31, 2 (1997), pp. 185-193. f) Lucrari referite in conferinte internationale: (in bold sunt evidentiati studentii mei) 42. T. Ahmed, G. DeLancy, A. Paun: A Case-Study on the Influence of Noise to Log-Gain Principles for Flux Dynamic Discovery. Int. Conf. on Membrane Computing 2012, Lecture Notes in Computer Science, vol. 7762, 2013, 88-100. 43. A. Paun, M. Sidoroff: Sequentiality Induced by Spike Number in SNP Systems: Small Universal Machines. Int. Conf. on Membrane Computing 2011: 333-345 44. A. Paun, M. Paun, A. Rodríguez-Patón, J. Jack: Poster: Biochemical signaling: A discrete simulation with memory enhancement. ICCABS 2011: 257 45. J. Jack, A.Paun: The Nondeterministic Waiting Time Algorithm: A Review DCFS 2009: 29-46 46. P. Sosík, A. Paun, A. Rodríguez-Patón, D. Pérez: On the Power of Computing with Proteins on Membranes. Workshop on Membrane Computing 2009: 448-460 47. O.H. Ibarra, A. Paun, A. Rodriguez-Paton, Sequentiality Induced by Spike Number in SNP Systems, Pre-proceedings of Fourteenth meeting on DNA Computing (DNA14), June 2-6, 2008, Prague, Czech Republic, pp. 36-47. 48. J. Jack, A. Paun, A. Rodriguez-Paton, Effects of HIV-1 Proteins on the Fas-Mediated Apoptotic Signaling Cascade: A Computational Study of Latent CD4+ T Cell Activation, accepted at Ninth Workshop on Molecular Computation, WMC9, Edinburgh (UK) July 28-31, 2008, 20pp. 49. A. Paun, M. Paun, A. Rodriguez-Paton, Hopcroft's minimization technique: queues or stacks?, CIAA 13, July 21-24, 2008, San Francisco, USA, Lecture Notes in Computer Science, Berlin, vol. 5148, 2008, pp. 78-91. 50. A. Paun, B. Popa, P Systems with Proteins on Membranes and Membrane Division, Proc of. Tenth International Conference Developments in Language Theory (DLT 2006), June 26-29, 2006, Santa Barbara, CA, USA, pp. 292-303 51. H. Nagda, A. Paun, A. Rodriguez-Paton, P Systems with Symport/Antiport and Time, Proc. of Workshop on Membrane Computing (at the crossroads of Cell Biology and Computing), WMC07, 17-21 July 2006, pp. 429-442 and also Lecture Notes in Computer Science, 4361, Berlin, (2006), pp. 463-476. 52. C. Campeanu, A. Paun, J. R. Smith, Tight Bounds for the State Complexity of Deterministic Cover Automata, Proc. of Descriptional Complexity of Formal Systems, 8th Workshop, June
21-23, 2006, Las Cruces, New Mexico, USA (9 pages). 53. M. Ionescu, A. Paun, Gh. Paun, M.J. Pérez-Jiménez, Computing with Spiking Neural P Systems: Traces and Small Universal Systems, Proc. of 12th Intern. Meeting on DNA Based Computers (DNA 2006), June 5-9, Seoul, Korea, pp. 1-16. 54. O.H. Ibarra, S. Woodworth, F. Yu, A. Paun, On Spiking Neural P Systems and Partially Blind Counter Machines. Proc. Of 5th International Conference on Unconventional Computation (UC 2006), 4th-8th September 2006, York, UK, pp. 113-129. 55. C. Campeanu, A. Paun, J. R. Smith, An Incremental Algorithm for Minimal Deterministic Finite Cover Automata, Proc. of Tenth International Conference on Implementation and Application of Automata (CIAA05), June 27 29, 2005, Sophia Antipolis, France, pp. 90-103; (the conference had approximately 30% acceptance rate) also in Lecture Notes in Computer Science, Berlin, Volume 3845/2006 pages 90-103. 56. O.H. Ibarra, A. Paun, Counting Time in Computing with Cells, Proc. of 11th Intern. Meeting on DNA Based Computers (DNA11), June 6-9, 2005, London Ontario, Canada, pp. 112-128, also in Lecture Notes in Computer Science, Volume 3892/2006, Berlin, pages 112-128. 57. C. Campeanu, A. Paun, NFA to DFCA Transformations For Binary Alphabets, Proc. of Ninth International Conference on Implementation and Application of Automata (CIAA 2004), Kingston, Canada (2004). 58. C. Campeanu, A. Paun, Lower Bounds for NFA to DFCA Transformations, Proc. of Descriptional Complexity of Formal Systems, 6th Workshop, London, Ontario, Canada (2004) (10 pages). 59. R. Freund, M. Oswald, A. Paun, Extended Gemmating P Systems are Computationally Complete with Four Membranes, Proc. of Descriptional Complexity of Formal Systems, 6th Workshop, London, Ontario, Canada (2004) (10 pages). 60. R. Freund, M. Oswald, A. Paun, P systems generating trees, Proc. of Workshop on Membrane Computing 2004 (WMC5), Milano, Italy, 2004, pp. 221-232 also in Lecture Notes in Computer Science, 3365, Berlin, (2004), pp. 309-319. 61. C. Campeanu, A. Paun, Computing Beyond the Turing Limit Using the H Systems, Proc. of the Tenth International Meeting on DNA Computing (DNA10), Milan, (2004), pp. 314-323 also in Lecture Notes in Computer Science, 3384, Berlin, (2005), pp. 24-34. 62. F. Bernardini, A. Paun, Universality of Minimal Symport/Antiport: Five Membranes Suffice, Lecture Notes in Computer Science, 2933, Berlin, (2004), pp. 43-54. 63. R. Freund, A. Paun, Membrane Systems with Symport/Antiport: Universality Results, Lecture Notes in Computer Science, 2597, Berlin, (2003), pp. 270-287. 64. M. Ionescu, C. Martín-Vide, A. Paun, Gh. Paun: Unexpected Universality Results for Three Classes of P Systems with Symport/Antiport. DNA 2002: LNCS, Volume 2568/2003, pp.281-290 65. C. Campeanu, A. Paun, The Number of Similarity Relations and the Number of Minimal Deterministic Finite Cover Automata, Proc. of 7th International Conference on Implementation and Application of Automata (CIAA 2002), Tours, France, 2002, pp. 71-80. 66. M. Ionescu, C. Martin-Vide, A. Paun, Gh. Paun, Membrane Systems with Symport/Antiport: (Unexpected) Universality Results, Proc. of 8th Intern. Meeting on DNA Based Computers (DNA8) (M. Hagiya, A. Obuchi, eds.), Hokkaido University, Sapporo, Japan, 2002, pp. 151-160. 67. A. Paun, P Systems with string-objects: Universality results, Proc. of Workshop on Membrane Computing (WMC-CdeA 2001), Curtea-de-Arges, Romania, 2001, pp. 229-242. 68. A. Paun, On P Systems with Global Rules. Proc. of 7th Intern. Meeting on DNA Based Computers (DNA7) (N. Jonoska, N.C. Seeman, eds.), Tampa, Florida, USA, 2001, pp. 43-52. 69. A. Paun, On P Systems with Active Membranes, Proc. of UMC2K, in Discrete Mathematics and Theoretical Computer Science, Springer (I. Antoniou, C.S. Calude, M.J. Dinneen,
eds.), Brussels, Belgium, 2000, pp. 187-201. 70. A. Paun, N. Santean, S. Yu, An O(n²) Algorithm for Constructing Minimal Cover Automata for Finite Languages, Proc. of Fifth International Conference on Implementation and Application of Automata (CIAA 2000) (M. Daley, M. Eramian, S. Yu, eds.), London, Ontario, 2000, pp. 233-241. 71. A. Paun, On the Diameter of Various Classes of H Systems, Proc. of Intern. Workshop on Descriptional Complexity of Automata, Grammars and Related Structures (DCAGRS '99) (J. Dassow, D. Wotschke, eds.), Magdeburg, Germany, 1999, pp. 165-174. 72. A. Paun, M. Paun, State and Transition Complexity of Watson-Crick Finite Automata, Proc. of Fundamentals of Computation Theory Conf. (FCT'99) Iasi, 1999, Lecture Notes in Computer Science, 1684, Springer-Verlag, Berlin, 1999, pp. 409-420. 73. A. Paun, M. Paun, Controlled and Distributed H Systems of a Small Radius, Computing with Bio-Molecules; Theory and Experiments, Springer, Singapore, 1998, pp. 239-254. g) Alte publicatii: 74. L. Kari, C. Martin-Vide, A. Paun, On the Universality of P Systems with Minimal Symport/Antiport Rules, Lecture Notes in Computer Science, 2950, Berlin, (2004), pp. 254-265. 75. R. Freund, A. Paun, P Systems with Active Membranes and without Polarizations, Dept. of Computer Sciences and Artificial Intelligence, Univ. of Sevilla Tech. Rep 01/2004, Second Brainstorming Week on Membrane Computing, Sevilla, Spain, Feb 2-7, 2004, pp. 193-205. 76. S.N. Krishna, A. Paun, Some Universality Results on Evolution-Communication P Systems, Rovira i Virgili Univ., Tech. Rep. No. 26, Brainstorming Week on Membrane Computing; Tarragona, 2003, pp. 207-215. 77. S.N. Krishna, A. Paun, Three Universality Results on P Systems, Rovira i Virgili Univ., Tech. Rep. No. 26, Brainstorming Week on Membrane Computing; Tarragona, 2003, pp. 198-206. 78. C. Martin-Vide, A. Paun, Gh. Paun, Membrane Computing: New Results, New Problems, Bulletin of the EATCS, 78 (2002), pp. 204-212. 79. L. Kari, A. Paun, String Operations Suggested by DNA Biochemistry: the Balanced Cut Operation, Words, Semigroups & Transductions (M. Ito, et. al., eds.), World Scientific, Singapore, 2001, pp. 275-287. 80. A. Paun, Gh. Paun, A. Rodriguez-Paton, Further Remarks on P Systems with Symport Rules, An. Stiint. Univ. Al. I. Cuza Iasi Inform. 10 (2001), pp. 3-18. 81. A. Paun, M. Paun, On the Membrane Computing Based on Splicing, Where Mathematics, Computer Science, Linguistics and Biology Meet (C. Martin-Vide, V. Mitrana, eds.), Kluwer, Dordrecht, 2001, pp. 409-422. 82. A. Paun, On Time-Varying H systems, Bulletin of the EATCS, 67 (1999), pp. 157-164.